Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A1 F2 I209 R1
|
216 |
14.4 |
815930 |
96.1% |
784108 |
85.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
950,036 |
(T)5→4 |
intergenic (‑114/+292) |
focA ← / ← ycaO |
formate transporter FocA/30S ribosomal protein S12 methylthiotransferase accessory factor YcaO |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 950,032 | 0 | T | . | 100.0%
| 23.9
/ NA
| 7 | intergenic (‑110/+296) | focA/ycaO | formate transporter FocA/30S ribosomal protein S12 methylthiotransferase accessory factor YcaO |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (4/3); total (4/3) |
GGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGTTTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATT > NZ_CP009273/949946‑950091
|
ggCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATAGtttt < 1:165074/90‑1 (MQ=255)
gagaTACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCaa < 1:267568/90‑1 (MQ=255)
cTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACgg < 1:200946/90‑1 (MQ=255)
aaGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTaaa > 2:22429/1‑90 (MQ=255)
tGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATc > 1:190158/1‑90 (MQ=255)
atatCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTa < 1:172075/57‑1 (MQ=255)
atatCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTa > 2:172075/1‑57 (MQ=255)
cGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAAtt > 1:109420/1‑90 (MQ=255)
|
GGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGTTTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATT > NZ_CP009273/949946‑950091
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGTTTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATT > NZ_CP009273/949946‑950091
|
GGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATAG‑TTTTATGCAAATAC < SRR3722091.167462/100‑1 (MQ=60)
GAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTA < SRR3722091.271916/100‑1 (MQ=60)
CTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATT < SRR3722091.203976/100‑1 (MQ=60)
cgtcagatgtgtataagagacagGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGAT < SRR3722091.174538/77‑1 (MQ=60)
GCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATC > SRR3722091.192964/1‑100 (MQ=60)
GATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGG‑TTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATT > SRR3722091.111094/1‑100 (MQ=60)
|
GGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGATATAGATCATATCTCGCCTGGCTTATAGGCCCGTAACTCGCATGGTTTTTATGCAAATACGGAGTAAATATTTGATTATCCAAATAAAAATAAATTTTAAAAATT > NZ_CP009273/949946‑950091
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
